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Re: Identifiers (was Notes from today's meeting)

From: Alasdair J G Gray <Alasdair.Gray@manchester.ac.uk>
Date: Tue, 4 Jun 2013 10:27:53 +0100
Cc: Jerven Bolleman <me@jerven.eu>, "public-semweb-lifesci@w3.org" <public-semweb-lifesci@w3.org>
Message-Id: <DE448DA9-5280-400C-9F40-E4B1E417EDAE@manchester.ac.uk>
To: Michel Dumontier <michel.dumontier@gmail.com>

On 3 Jun 2013, at 17:51, Michel Dumontier <michel.dumontier@gmail.com> wrote:

> Also continuing the discussion on e-mail that started on the call.
> We should have a clear definition of data item if we are going to record information about such things. e.g. baseURI, what happens if we have 2 data item types in a single dataset?
> ultimately, what i want is to :
> i) to validate the syntax of identifier in some dataset or cross reference (legacy, RDF)

This is a good goal.

> ii) to compose a URI from a preferred or alternative prefix and an identifier   (legacy to RDF)

This is problematic. Prefixes do not have any global scope. A prefix in an XML or turtle file MUST be defined within that file; it is a locally scoped variable; ultimately it is syntactic sugar. While I appreciate that something like PMID:22434840 has meaning to folk in the life sciences field, it is problematic if it is written out of context and ultimately it is not machine understandable. The only way such an identifier is useful is if it has a definition in the document with it for the value of the locally scoped PMID, and then in that case I could equally have used foo:22434840.

> iii) to decompose a URI to a preferred prefix and identifier pair (RDF to legacy)

Again, there is a scoping problem. Prefixes are locally scoped and must be defined.

> iv) to translate one URI pattern to another URI pattern (RDF)

This is an important problem and is where services such as BridgeDB and Identifiers.org come into the mix. There are some nuances that must be captured even if we are only focusing on RDF URIs (and not the URIs of web pages associate with a resource which opens up another can of worms). For example, some representations of ChEBI use identifiers of the form foo:CHEBI:73726 while others use bar:CHEBI_73726.

What we need to remember here is that these are optional (MAY) properties.


Dr Alasdair J G Gray
Research Associate
+44 161 275 0145


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Received on Tuesday, 4 June 2013 09:28:05 UTC

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